com.actelion.research.orbit.imageAnalysis.dal.ScaleoutSpark Maven / Gradle / Ivy
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/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see
* key: Orbit.samba.share
*/
protected IRemoteContextStore createContextStore() {
try {
String user = "";
String password = "";
String domain = "";
String share = "";
String[] smbArr = new String[4];
Properties sparkConfProps = getProperties();
String smb = sparkConfProps.getProperty(sparkPropertiesKey);
if (smb != null && smb.length() > 0)
smbArr = parseSMBurl(smb);
domain = smbArr[0];
user = smbArr[1];
password = smbArr[2];
share = smbArr[3];
if (password == null || password.length() == 0) password = null;
if (domain == null || domain.length() == 0) domain = null;
return new SmbUtils(user, password, domain, share);
} catch (IOException e) {
e.printStackTrace();
}
return null;
}
private Properties getProperties() throws IOException {
Properties sparkConfProps = new Properties();
File sparkConfPropsFile = new File(getSparkConfFilename());
if (sparkConfPropsFile.exists()) {
sparkConfProps.load(new FileReader(sparkConfPropsFile));
} else {
DALConfig.readConfigProperties(sparkConfProps);
}
return sparkConfProps;
}
/**
* At least a share must be specified. Domain and user and password are optional.
*
* @param SMBurl, e.g. domain/user:password@smb://server/share
* @return [domain, user, password, smb share]
*/
public String[] parseSMBurl(String SMBurl) {
try {
String user = "";
String password = "";
String domain = "";
String share = "";
String[] split = SMBurl.split("@");
if (split.length == 1) { // no domain,user,password
return new String[]{null, null, null, SMBurl.trim()};
}
share = split[1].trim();
if (split[0].contains(":")) {
split = split[0].split(":");
password = split[1].trim();
}
if (split[0].contains("/")) {
split = split[0].split("/");
domain = split[0].trim();
user = split[1].trim();
} else {
user = split[0].trim();
}
return new String[]{domain, user, password, share};
} catch (Exception e) {
throw new IllegalArgumentException("SMBurl is nto in the form 'domain/user:password@smb://server/share'");
}
}
@Override
public IMapReduceExecutor createMapReduceExecutor(IMapReduce mapReduce) {
try {
// String[] jars = new String[]{};
String[] jars = buildJarList(DALConfig.getLibDir());
Class[] paramString = new Class[]{String.class};
Class[] paramStringArr = new Class[]{String[].class};
IMapReduceExecutor executor = (IMapReduceExecutor) Class.forName("com.actelion.research.mapReduceExecSpark.executors.MapReduceExecutorSpark").newInstance();
Object sparkConf = createSparkConf();
if (sparkConf != null) {
executor.getClass().getDeclaredMethod("setSparkConf", Class.forName("org.apache.spark.SparkConf")).invoke(executor, sparkConf);
executor.getClass().getDeclaredMethod("setJars", paramStringArr).invoke(executor, new Object[]{jars});
executor.getClass().getDeclaredMethod("setResultSaver", IRemoteContextStore.class, String.class).invoke(executor, getRemoteContextStore(), "spark");
} else {
String userDir = System.getProperty("user.dir");
logger.info("no " + userDir + File.separator + "SparkConf.properties found. However, master and appName will be set.");
logger.info("To define more specific SparkConf parameters, please create a SparkConf.properties file. The parameters are documented here: http://spark.apache.org/docs/latest/configuration.html");
logger.info("Spark master: " + master);
logger.info("Spark appName: " + appName);
executor.getClass().getDeclaredMethod("setMaster", paramString).invoke(executor, new String(master));
executor.getClass().getDeclaredMethod("setAppName", paramString).invoke(executor, new String(appName));
executor.getClass().getDeclaredMethod("setJars", paramStringArr).invoke(executor, new Object[]{jars});
executor.getClass().getDeclaredMethod("setResultSaver", IRemoteContextStore.class, String.class).invoke(executor, getRemoteContextStore(), "spark");
}
return executor;
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException("class com.actelion.research.mapReduceExecSpark.executors.MapReduceExecutorSpark not found");
}
}
private Object createSparkConf() throws Exception {
// trying to read SparkConf.properties in execution directory
File sparkConfPropsFile = new File(getSparkConfFilename());
if (sparkConfPropsFile.exists()) {
logger.info("using Spark config properties from " + sparkConfPropsFile.getAbsolutePath() + " (JARs will be set in addition)");
Object sparkConf = Class.forName("org.apache.spark.SparkConf").newInstance();
Properties sparkConfProps = new Properties();
sparkConfProps.load(new FileReader(sparkConfPropsFile));
for (Object key : sparkConfProps.keySet()) {
String keyStr = String.valueOf(key);
if (keyStr != null) {
String val = sparkConfProps.getProperty(keyStr);
if (val != null) {
if (!keyStr.toLowerCase().startsWith("orbit")) { // e.g. samba configuration starts with Orbit
logger.info("setting Spark config property: " + keyStr + ": " + val);
sparkConf.getClass().getDeclaredMethod("set", String.class, String.class).invoke(sparkConf, keyStr, val);
}
}
}
}
return sparkConf;
}
return null;
}
private String getSparkConfFilename() {
File sparkConfPropsFile = new File(sparkPropertiesFilename);
if (sparkConfPropsFile.exists()) return sparkConfPropsFile.getAbsolutePath();
sparkConfPropsFile = new File(System.getProperty("user.home") + File.separator + sparkPropertiesFilename);
if (sparkConfPropsFile.exists()) return sparkConfPropsFile.getAbsolutePath();
return sparkPropertiesFilename;
}
@Override
public IRemoteContextStore getRemoteContextStore() {
if (remoteContextStore == null) {
remoteContextStore = createContextStore();
}
return remoteContextStore;
}
@Override
public int getParallelism() {
Properties props = null;
try {
props = getProperties();
String p = props.getProperty(sparkDefaultParallelism);
if (p != null && p.length() > 0) {
int parallelism = Integer.parseInt(p.trim());
logger.info("orbit scaleout parallelism: " + parallelism);
return parallelism;
}
} catch (IOException e) {
e.printStackTrace();
}
return 100;
}
@Override
public JInternalFrame createExistingResultView() throws Exception {
/*
JInternalFrame frame = new JInternalFrame("Existing Results");
JLabel label = new JLabel("Not implemented for this Scaleout implementation.\nPlease use the Spark web frontend to view and manage running tasks.");
label.setFont(label.getFont().deriveFont(32));
frame.add(label);
frame.pack();
return frame;
*/
return new SambaMRResultsView();
}
/**
* lists all jars in /lib but excludes some (hopefully) not needed jars
*/
public String[] buildJarList(String libDir) {
FilenameFilter filter = new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
String n = name.toLowerCase();
if (n.startsWith("hadoop")) return false;
if (n.startsWith("spark")) return false;
if (n.startsWith("javax")) return false;
if (n.startsWith("spring")) return false;
if (n.startsWith("akka")) return false;
if (n.startsWith("jersey")) return false;
if (n.startsWith("asm-")) return false;
if (n.startsWith("hibernate")) return false;
if (n.startsWith("zookeeper")) return false;
if (n.startsWith("substance")) return false;
if (n.startsWith("trident")) return false;
if (n.startsWith("scala")) return false;
if (n.startsWith("jackson")) return false;
if (n.startsWith("pdfbox")) return false;
if (n.startsWith("tachyon")) return false;
if (n.startsWith("velocity")) return false;
if (n.startsWith("jhdf5")) return false;
if (n.startsWith("xalan")) return false;
if (n.startsWith("netty")) return false;
return n.endsWith(".jar");
}
};
List strList = new ArrayList<>();
File dir = new File(libDir);
for (File f : dir.listFiles(filter)) {
strList.add(f.getAbsolutePath());
}
File orbitFile1 = new File(libDir + "/../orbit-image-analysis.jar");
if (orbitFile1.exists()) {
strList.add(orbitFile1.getAbsolutePath());
}
File orbitFile2 = new File(libDir + "/../OrbitImageAnalysis.jar");
if (orbitFile2.exists()) {
strList.add(orbitFile2.getAbsolutePath());
}
return strList.toArray(new String[0]);
}
public String getAppName() {
return appName;
}
public void setAppName(String appName) {
this.appName = appName;
}
public String getMaster() {
return master;
}
public void setMaster(String master) {
this.master = master;
}
public static void main(String[] args) throws URISyntaxException, UnsupportedEncodingException {
ScaleoutSpark so = new ScaleoutSpark();
for (String s : so.buildJarList(DALConfig.getLibDir())) {
System.out.println(s);
}
}
}